Abstract: By analyzing the status of water quality, the community structure and the characteristic index of phytoplankton in Meizhou Bay, it has been concluded that, presently, Meizhou Bay is still under light pollution and low trophic level. However, the discharging of organic pollutants to the middle and inner parts of Meizhou Bay has caused the changing of structure and stability of phytoplankton community and may lead to the arising of eutrophication and red tides.